Abstract

Abstract Summary The Genome Taxonomy Database Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the GTDB. GTDB-Tk is computationally efficient and able to classify thousands of draft genomes in parallel. Here we demonstrate the accuracy of the GTDB-Tk taxonomic assignments by evaluating its performance on a phylogenetically diverse set of 10 156 bacterial and archaeal metagenome-assembled genomes. Availability and implementation GTDB-Tk is implemented in Python and licenced under the GNU General Public Licence v3.0. Source code and documentation are available at: https://github.com/ecogenomics/gtdbtk. Supplementary information Supplementary data are available at Bioinformatics online.

Keywords

Python (programming language)GenomeMetagenomicsDocumentationMIT LicenseTaxonomy (biology)Source codeComputer scienceComputational biologyBacterial genome sizeBiologySoftwareProgramming languageGeneticsGene

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Publication Info

Year
2019
Type
article
Volume
36
Issue
6
Pages
1925-1927
Citations
4811
Access
Closed

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Pierre-Alain Chaumeil, Aaron J. Mussig, Philip Hugenholtz et al. (2019). GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics , 36 (6) , 1925-1927. https://doi.org/10.1093/bioinformatics/btz848

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DOI
10.1093/bioinformatics/btz848